[SciPy-Dev] SciPy 0.11.0 Failures in scipy.test()

Wim R. Cardoen wcardoen@gmail....
Wed Apr 3 10:00:54 CDT 2013


Hello,

This morning I installed numpy 1.7.0 and ran its test suite successfully.
After installing scipy 0.11.0 I ran the scipy test suite and obtained a
bunch of failures. (see below #2).

I compiled the source code on the a RHEL6 box using gfortran (GNU Fortran
(GCC) 4.4.6)
as well as gcc (gcc (GCC) 4.4.6)
I used the OS's blas and lapack library and compiled suitesparse myself.
Do you have any idea how can I resolve these failures?

Thanks,

Wim

#1: Configuration to compile scipy 0.11.0
------------------------------------------------------------------------------------------------------------------------------------
 import scipy
>>> scipy.show_config()
blas_info:
    libraries = ['blas', 'lapack']
    library_dirs = ['/usr/lib64']
    language = f77
amd_info:
    libraries = ['amd']
    library_dirs = ['/uufs/chpc.utah.edu/sys/pkg/suitesparse/4.0.2_rhel6/lib
']
    define_macros = [('SCIPY_AMD_H', None)]
    swig_opts = ['-I/uufs/
chpc.utah.edu/sys/pkg/suitesparse/4.0.2_rhel6/include']
    include_dirs = ['/uufs/
chpc.utah.edu/sys/pkg/suitesparse/4.0.2_rhel6/include']
lapack_info:
    libraries = ['lapack', 'lapack']
    library_dirs = ['/usr/lib64']
    language = f77
atlas_threads_info:
  NOT AVAILABLE
blas_opt_info:
    libraries = ['blas', 'lapack', 'lapack']
    library_dirs = ['/usr/lib64']
    language = f77
    define_macros = [('NO_ATLAS_INFO', 1)]
atlas_blas_threads_info:
  NOT AVAILABLE
umfpack_info:
    libraries = ['umfpack', 'amd']
    library_dirs = ['/uufs/chpc.utah.edu/sys/pkg/suitesparse/4.0.2_rhel6/lib
']
    define_macros = [('SCIPY_UMFPACK_H', None), ('SCIPY_AMD_H', None)]
    swig_opts = ['-I/uufs/
chpc.utah.edu/sys/pkg/suitesparse/4.0.2_rhel6/include', '-I/uufs/
chpc.utah.edu/sys/pkg/suitesparse/4.0.2_rhel6/include']
    include_dirs = ['/uufs/
chpc.utah.edu/sys/pkg/suitesparse/4.0.2_rhel6/include']
lapack_opt_info:
    libraries = ['lapack', 'lapack', 'blas', 'lapack', 'lapack']
    library_dirs = ['/usr/lib64']
    language = f77
    define_macros = [('NO_ATLAS_INFO', 1)]
atlas_info:
  NOT AVAILABLE
lapack_mkl_info:
  NOT AVAILABLE
blas_mkl_info:
  NOT AVAILABLE
atlas_blas_info:
  NOT AVAILABLE
mkl_info:
  NOT AVAILABLE
--------------------------------------------------------------------------------------------------------------------------------------


#2: Failures after executing the
command
import scipy
scipy.test()

------------------------------
-------------------------------------------------------------------------------------------------------------
======================================================================
FAIL: test_arpack.test_symmetric_modes(True, <std-symmetric>, 'f', 2, 'LM',
None, 0.5, <class 'scipy.sparse.csr.csr_matrix'>, None, 'normal')
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/uufs/
chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/nose-1.1.2-py2.7.egg/nose/case.py",
line 197, in runTest
    self.test(*self.arg)
  File "/uufs/
chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py",
line 257, in eval_evec
    assert_allclose(LHS, RHS, rtol=rtol, atol=atol, err_msg=err)
  File "/uufs/
chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/numpy/testing/utils.py",
line 1179, in assert_allclose
    verbose=verbose, header=header)
  File "/uufs/
chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/numpy/testing/utils.py",
line 645, in assert_array_compare
    raise AssertionError(msg)
AssertionError:
Not equal to tolerance rtol=0.00178814, atol=0.000357628
error for eigsh:standard, typ=f, which=LM, sigma=0.5, mattype=csr_matrix,
OPpart=None, mode=normal
(mismatch 100.0%)
 x: array([[  2.38156418e-01,  -6.75444982e+09],
       [ -1.07853470e-01,  -8.01245676e+09],
       [  1.24683023e-01,  -5.19757686e+09],...
 y: array([[  2.38156418e-01,  -5.70949789e+08],
       [ -1.07853470e-01,  -4.05829392e+08],
       [  1.24683023e-01,   6.25800146e+07],...

======================================================================
FAIL: test_arpack.test_symmetric_modes(True, <std-symmetric>, 'f', 2, 'LM',
None, 0.5, <class 'scipy.sparse.csr.csr_matrix'>, None, 'buckling')
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/uufs/
chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/nose-1.1.2-py2.7.egg/nose/case.py",
line 197, in runTest
    self.test(*self.arg)
  File "/uufs/
chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py",
line 257, in eval_evec
    assert_allclose(LHS, RHS, rtol=rtol, atol=atol, err_msg=err)
  File "/uufs/
chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/numpy/testing/utils.py",
line 1179, in assert_allclose
    verbose=verbose, header=header)
  File "/uufs/
chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/numpy/testing/utils.py",
line 645, in assert_array_compare
    raise AssertionError(msg)
AssertionError:
Not equal to tolerance rtol=0.00178814, atol=0.000357628
error for eigsh:standard, typ=f, which=LM, sigma=0.5, mattype=csr_matrix,
OPpart=None, mode=buckling
(mismatch 100.0%)
 x: array([[  3.53755447e-01,  -2.29114355e+04],
       [ -1.60204595e-01,  -6.65625445e+04],
       [  1.85203065e-01,  -2.69012500e+04],...
 y: array([[  3.53755447e-01,  -8.88255444e+05],
       [ -1.60204595e-01,  -2.39343354e+06],
       [  1.85203065e-01,  -3.96842525e+04],...

======================================================================
FAIL: test_arpack.test_symmetric_modes(True, <std-symmetric>, 'f', 2, 'LM',
None, 0.5, <class 'scipy.sparse.csr.csr_matrix'>, None, 'cayley')
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/uufs/
chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/nose-1.1.2-py2.7.egg/nose/case.py",
line 197, in runTest
    self.test(*self.arg)
  File "/uufs/
chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py",
line 257, in eval_evec
    assert_allclose(LHS, RHS, rtol=rtol, atol=atol, err_msg=err)
  File "/uufs/
chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/numpy/testing/utils.py",
line 1179, in assert_allclose
    verbose=verbose, header=header)
  File "/uufs/
chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/numpy/testing/utils.py",
line 645, in assert_array_compare
    raise AssertionError(msg)
AssertionError:
Not equal to tolerance rtol=0.00178814, atol=0.000357628
error for eigsh:standard, typ=f, which=LM, sigma=0.5, mattype=csr_matrix,
OPpart=None, mode=cayley
(mismatch 100.0%)
 x: array([[ -2.38156418e-01,   1.04661597e+09],
       [  1.07853470e-01,   1.39930271e+09],
       [ -1.24683023e-01,   9.56906461e+08],...
 y: array([[ -2.38156418e-01,   7.63721281e+07],
       [  1.07853470e-01,   1.25169905e+08],
       [ -1.24683023e-01,   2.91283130e+07],...

======================================================================
FAIL: test_arpack.test_symmetric_modes(True, <std-symmetric>, 'f', 2, 'LM',
None, 0.5, <function asarray at 0xd19a28>, None, 'normal')
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/uufs/
chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/nose-1.1.2-py2.7.egg/nose/case.py",
line 197, in runTest
    self.test(*self.arg)
  File "/uufs/
chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py",
line 257, in eval_evec
    assert_allclose(LHS, RHS, rtol=rtol, atol=atol, err_msg=err)
  File "/uufs/
chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/numpy/testing/utils.py",
line 1179, in assert_allclose
    verbose=verbose, header=header)
  File "/uufs/
chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/numpy/testing/utils.py",
line 645, in assert_array_compare
    raise AssertionError(msg)
AssertionError:
Not equal to tolerance rtol=0.000357628, atol=0.000357628
error for eigsh:standard, typ=f, which=LM, sigma=0.5, mattype=asarray,
OPpart=None, mode=normal
(mismatch 100.0%)
 x: array([[ -2.38157020e-01,  -9.38079485e+09],
       [  1.07853829e-01,  -1.09927593e+10],
       [ -1.24683096e-01,  -7.26035649e+09],...
 y: array([[ -2.38157028e-01,  -1.14406333e+09],
       [  1.07853849e-01,  -1.61444148e+09],
       [ -1.24683097e-01,  -9.66750843e+08],...

======================================================================
FAIL: test_arpack.test_symmetric_modes(True, <std-symmetric>, 'f', 2, 'LM',
None, 0.5, <function asarray at 0xd19a28>, None, 'buckling')
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/uufs/
chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/nose-1.1.2-py2.7.egg/nose/case.py",
line 197, in runTest
    self.test(*self.arg)
  File "/uufs/
chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py",
line 257, in eval_evec
    assert_allclose(LHS, RHS, rtol=rtol, atol=atol, err_msg=err)
  File "/uufs/
chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/numpy/testing/utils.py",
line 1179, in assert_allclose
    verbose=verbose, header=header)
  File "/uufs/
chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/numpy/testing/utils.py",
line 645, in assert_array_compare
    raise AssertionError(msg)
AssertionError:
Not equal to tolerance rtol=0.000357628, atol=0.000357628
error for eigsh:standard, typ=f, which=LM, sigma=0.5, mattype=asarray,
OPpart=None, mode=buckling
(mismatch 100.0%)
 x: array([[  3.53756177e-01,   3.54742236e+05],
       [ -1.60205036e-01,   9.37802669e+05],
       [  1.85203150e-01,  -6.91305082e+04],...
 y: array([[  3.53756197e-01,   1.19154973e+07],
       [ -1.60205063e-01,   3.16087279e+07],
       [  1.85203158e-01,  -2.15500940e+06],...

======================================================================
FAIL: test_arpack.test_symmetric_modes(True, <std-symmetric>, 'f', 2, 'LM',
None, 0.5, <function asarray at 0xd19a28>, None, 'cayley')
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/uufs/
chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/nose-1.1.2-py2.7.egg/nose/case.py",
line 197, in runTest
    self.test(*self.arg)
  File "/uufs/
chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py",
line 257, in eval_evec
    assert_allclose(LHS, RHS, rtol=rtol, atol=atol, err_msg=err)
  File "/uufs/
chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/numpy/testing/utils.py",
line 1179, in assert_allclose
    verbose=verbose, header=header)
  File "/uufs/
chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/numpy/testing/utils.py",
line 645, in assert_array_compare
    raise AssertionError(msg)
AssertionError:
Not equal to tolerance rtol=0.000357628, atol=0.000357628
error for eigsh:standard, typ=f, which=LM, sigma=0.5, mattype=asarray,
OPpart=None, mode=cayley
(mismatch 100.0%)
 x: array([[ -2.38156244e-01,   3.27365597e+08],
       [  1.07853608e-01,   4.31395993e+08],
       [ -1.24682902e-01,   2.93518385e+08],...
 y: array([[ -2.38156393e-01,   2.20001033e+07],
       [  1.07853475e-01,   3.05206768e+07],
       [ -1.24683015e-01,   8.50334431e+06],...
======================================================================
FAIL: test_arpack.test_symmetric_modes(True, <std-symmetric>, 'f', 2, 'SM',
None, 0.5, <class 'scipy.sparse.csr.csr_matrix'>, None, 'buckling')
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/uufs/
chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/nose-1.1.2-py2.7.egg/nose/case.py",
line 197, in runTest
    self.test(*self.arg)
  File "/uufs/
chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py",
line 257, in eval_evec
    assert_allclose(LHS, RHS, rtol=rtol, atol=atol, err_msg=err)
  File "/uufs/
chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/numpy/testing/utils.py",
line 1179, in assert_allclose
    verbose=verbose, header=header)
  File "/uufs/
chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/numpy/testing/utils.py",
line 645, in assert_array_compare
    raise AssertionError(msg)
AssertionError:
Not equal to tolerance rtol=0.00178814, atol=0.000357628
error for eigsh:standard, typ=f, which=SM, sigma=0.5, mattype=csr_matrix,
OPpart=None, mode=buckling
(mismatch 100.0%)
 x: array([[  3.32810915e-02,  -1.39781114e+06],
       [  8.83144107e-02,   6.75649002e+05],
       [ -5.86642416e-03,  -6.19039713e+05],...
 y: array([[  3.32810915e-02,  -2.24275052e+05],
       [  8.83144107e-02,   1.08299209e+05],
       [ -5.86642416e-03,  -9.86191556e+04],...

======================================================================
FAIL: test_arpack.test_symmetric_modes(True, <std-symmetric>, 'f', 2, 'SM',
None, 0.5, <class 'scipy.sparse.csr.csr_matrix'>, None, 'cayley')
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/uufs/
chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/nose-1.1.2-py2.7.egg/nose/case.py",
line 197, in runTest
    self.test(*self.arg)
  File "/uufs/
chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py",
line 257, in eval_evec
    assert_allclose(LHS, RHS, rtol=rtol, atol=atol, err_msg=err)
  File "/uufs/
chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/numpy/testing/utils.py",
line 1179, in assert_allclose
    verbose=verbose, header=header)
  File "/uufs/
chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/numpy/testing/utils.py",
line 645, in assert_array_compare
    raise AssertionError(msg)
AssertionError:
Not equal to tolerance rtol=0.00178814, atol=0.000357628
error for eigsh:standard, typ=f, which=SM, sigma=0.5, mattype=csr_matrix,
OPpart=None, mode=cayley
(mismatch 100.0%)
 x: array([[  3.87506792e-03,   4.25513135e+07],
       [  1.02828460e-02,  -1.78393819e+07],
       [ -6.83054282e-04,  -3.54143274e+07],...
 y: array([[  3.87506792e-03,   2.90700178e+08],
       [  1.02828460e-02,  -1.18728352e+08],
       [ -6.83054282e-04,  -2.87462041e+08],...

======================================================================
.......


======================================================================
FAIL: test_arpack.test_symmetric_modes(True, <gen-symmetric>, 'd', 2, 'SA',
None, 0.5, <function asarray at 0xd19a28>, None, 'cayley')
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/uufs/
chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/nose-1.1.2-py2.7.egg/nose/case.py",
line 197, in runTest
    self.test(*self.arg)
  File "/uufs/
chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py",
line 257, in eval_evec
    assert_allclose(LHS, RHS, rtol=rtol, atol=atol, err_msg=err)
  File "/uufs/
chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/numpy/testing/utils.py",
line 1179, in assert_allclose
    verbose=verbose, header=header)
  File "/uufs/
chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/numpy/testing/utils.py",
line 645, in assert_array_compare
    raise AssertionError(msg)
AssertionError:
Not equal to tolerance rtol=4.44089e-13, atol=4.44089e-13
error for eigsh:general, typ=d, which=SA, sigma=0.5, mattype=asarray,
OPpart=None, mode=cayley
(mismatch 100.0%)
 x: array([[-0.36892684, -0.01935691],
       [-0.26850996, -0.11053158],
       [-0.40976156, -0.13223572],...
 y: array([[-0.43633077, -0.01935691],
       [-0.25161386, -0.11053158],
       [-0.36756684, -0.13223572],...

----------------------------------------------------------------------
Ran 5481 tests in 75.399s

FAILED (KNOWNFAIL=15, SKIP=41, failures=63)
Running unit tests for scipy
NumPy version 1.7.0
NumPy is installed in /uufs/
chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/numpy
SciPy version 0.11.0
SciPy is installed in /uufs/
chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/scipy
Python version 2.7.3 (default, Mar 28 2013, 15:20:19) [GCC 4.4.6 20120305
(Red Hat 4.4.6-4)]
nose version 1.1.2
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